Abstract

Genome-based phylogeny plays a central role in the future taxonomy and phylogenetics of Bacteria and Archaea by replacing 16S rRNA gene phylogeny. The concatenated core gene alignments are frequently used for such a purpose. The bacterial core genes are defined as single-copy, homologous genes that are present in most of the known bacterial species. There have been several studies describing such a gene set, but the number of species considered was rather small. Here we present the up-to-date bacterial core gene set, named UBCG, and software suites to accommodate necessary steps to generate and evaluate phylogenetic trees. The method was successfully used to infer phylogenomic relationship of Escherichia and related taxa and can be used for the set of genomes at any taxonomic ranks of Bacteria. The UBCG pipeline and file viewer are freely available at https://www.ezbiocloud.net/tools/ubcg and https://www.ezbiocloud.net/tools/ubcg_viewer , respectively.

Keywords

Phylogenetic treeBiologyPhylogeneticsPhylogenomicsGenomeArchaeaGeneComputational biologyBacterial genome sizeEvolutionary biologyGeneticsClade

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Publication Info

Year
2018
Type
article
Volume
56
Issue
4
Pages
280-285
Citations
1328
Access
Closed

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Seong-In Na, Yeong Ouk Kim, Seok-Hwan Yoon et al. (2018). UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. The Journal of Microbiology , 56 (4) , 280-285. https://doi.org/10.1007/s12275-018-8014-6

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DOI
10.1007/s12275-018-8014-6